Anil Wipat

Bi-level diversity optimisation for representative protein panel selection

This paper introduces a bi-level diversity-optimization framework for selecting representative protein panels, reducing redundancy and improving diversity compared to existing methods.

ro-crate-rs: Development of a Lightweight RO-Crate Rust Library for Automated Synthetic Biology

This paper introduces ro-crate-rs, a Rust library for creating RO-Crates to manage synthetic biology data, enabling FAIR compliance and reproducibility in automated workflows.

Engineering genetic circuits in receiver cells for diffusion-based molecular data communications

The paper designs a diffusion-based molecular communication system using synthetic genetic circuits and introduces a tool to optimize communication parameters for efficient cellular signal transmission.

Transcriptional Biomarker Discovery Towards Building A Load Stress Reporting System for Engineered Escherichia coli Strains

The paper identifies gene biomarkers to detect load stress in engineered E. coli strains using machine learning.

A knowledge integration strategy for the selection of a robust multi-stress biomarkers panel for Bacillus subtilis

This paper develops a computational method to select a robust gene expression biomarker panel for stress sensing in Bacillus subtilis using machine learning, gene regulatory networks, and co-expression networks.

A network approach to genetic circuit designs

The paper introduces a network-based method to represent genetic circuit designs, enabling better visualization and integration with other biological networks.

Integration of probabilistic functional networks without an external Gold Standard

The paper introduces ssNet, a method to integrate probabilistic functional networks without an external Gold Standard, showing comparable performance using Saccharomyces cerevisiae data.

Virtual Parts Repository 2: Model-driven design of genetic regulatory circuits

The paper introduces Virtual Parts Repository 2, a resource for model-driven design of genetic regulatory circuits, providing modular and reusable models and a rule-based abstraction for scalable simulations.

Essentially leading antibody production: An investigation of amino acids, myeloma and natural V-region signal peptides in producing Pertuzumab and Trastuzumab variants

The paper investigates how varying signal peptides and amino acid counts affect recombinant antibody production rates in HEK293 cells, developing a predictive model for transient production.

Capturing Multicellular System Designs Using the Synthetic Biology Open Language (SBOL)

The paper demonstrates how the SBOL standard can represent multicellular biological systems, enabling better sharing of complex designs across multiple cells.

Codon optimisation for maximising gene expression in multiple species and microbial consortia

The paper develops an evolutionary algorithm to optimise coding sequences for multiple organisms, showing it can outperform single-organism optimisation in some cases.

The Gene-Rich Genome of the Scallop Pecten maximus

The paper reports the high-quality genome assembly of Pecten maximus, revealing gene duplicates and highlighting Nav1 as a candidate for toxin resistance.

SBOL Visual 2 Ontology

The paper introduces the SBOL Visual 2 Ontology to standardize the mapping of genetic elements to visual glyphs, facilitating tool development and integration with biological standards.

Functional Analysis of Enzyme Families Using Residue-Residue Coevolution Similarity Networks

The paper introduces Coevolution Similarity Networks (CSNs) to analyze enzyme families by clustering based on coevolution patterns, showing higher predictive power for substrate specificity annotation than Sequence Similarity Networks.

SBOL-OWL: An ontological approach for formal and semantic representation of synthetic genetic circuits

The paper introduces SBOL-OWL, an ontology that enables machine-readable semantic representation of synthetic genetic circuits, enhancing computational tools' ability to understand and validate designs.

BacilloFlex: A modular DNA assembly toolkit for Bacillus subtilis synthetic biology

BacilloFlex provides a modular DNA assembly toolkit for B. subtilis synthetic biology, enabling rapid construction and integration of genetic circuits.